RT Journal Article
SR Electronic
T1 Comparative transcriptomics provides insight into the evolution of cold response in Pooideae
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 151431
DO 10.1101/151431
A1 Lars Grønvold
A1 Marian Schubert
A1 Simen R. Sandve
A1 Siri Fjellheim
A1 Torgeir R. Hvidsten
YR 2017
UL http://biorxiv.org/content/early/2017/10/12/151431.abstract
AB Background Understanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but conserved cold-response genes that might have played a role in the cold adaptation to temperate climate remain unidentified.Results To establish if molecular responses to cold are conserved throughout the Pooideae phylogeny, we assembled the transcriptomes of five species spanning early to later diverging lineages, and compared short-and long-term cold response in orthologous genes based on gene expression data. We confirmed that most genes previously identified as cold responsive in barley also responded to cold in our barley experiment. Interestingly, comparing cold response across the lineages using 8633 high confidence ortholog groups revealed that nearly half of all cold responsive genes were species specific and more closely related species did not share higher numbers of cold responsive genes than more distantly related species. Also, the previously identified cold-responsive barley genes displayed low conservation of cold response across species. Nonetheless, more genes than expected by chance shared cold response, both based on previously studied genes and based on the high confidence ortholog groups. Noticeable, all five species shared short-term cold response in nine general stress genes as well as the ability to down-regulate the photosynthetic machinery during cold temperatures.Conclusions We observed widespread lineage specific cold response in genes with conserved sequence across the Pooideae phylogeny. This is consistent with phylogenetic dating and historic temperature data which suggest that selection pressure resulting from dramatic global cooling must have acted on already diverged lineages. To what degree lineage specific evolution acted primarily through gain or loss of cold response remains unclear, however, phylogeny-wide conservation of certain genes and processes indicated that the last common ancestor may have possessed some cold response.